A probabilistic transmission and population dynamic model to assess tuberculosis infection risk

Genomic transmission clusters and circulating lineages of Mycobacterium tuberculosis among refugees residing in refugee camps in Ethiopia

BACKGROUND

Understanding the transmission dynamics of Mycobacterium tuberculosis (Mtb) could benefit the design of tuberculosis (TB) prevention and control strategies for refugee populations. Whole Genome Sequencing (WGS) has not yet been used to document the Mtb transmission dynamics among refugees in Ethiopia. We applied WGS to accurately identify transmission clusters and Mtb lineages among TB cases in refugee camps in Ethiopia.

METHOD AND DESIGN

We conducted a cross-sectional study of 610 refugees in refugee camps in Ethiopia presenting with symptoms of TB. WGS data of 67 isolates was analyzed using the Maximum Accessible Genome for Mtb Analysis (MAGMA) pipeline; iTol and FigTree were used to visualize phylogenetic trees, lineages, and the presence of transmission clusters.

RESULTS

Mtb culture-positive refugees originated from South Sudan (52/67, 77.6%), Somalia (9/67, 13.4%). Eritrea (4/67, 6%), and Sudan (2/67, 3%). The majority (52, 77.6%) of the isolates belonged to Mtb lineage (L) 3, and one L9 was identified from a Somalian refugee. The vast majority (82%) of the isolates were pan-susceptible Mtb, and none were multi-drug-resistant (MDR)-TB. Based on the 5-single nucleotide polymorphisms cutoff, we identified eight potential transmission clusters containing 23.9% of the isolates. Contact investigation confirmed epidemiological links with either family or social interaction within the refugee camps or with neighboring refugee camps.

CONCLUSION

Four lineages (L1, L3, L4, and L9) were identified, with the majority of strains being L3, reflecting the Mtb L3 dominance in South Sudan, where the majority of refugees originated from. Recent transmission among refugees was relatively low (24%), likely due to the short study period. The improved understanding of the Mtb transmission dynamics using WGS in refugee camps could assist in designing effective TB control programs for refugees.

Assessment of Comorbidity in Patients with Drug-Resistant Tuberculosis

A wide range of comorbidities, especially in multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) patients, markedly complicates selecting effective treatment of tuberculosis (TB) and preventing the development of adverse events. At present, it is impossible to assess the severity of comorbid pathologies and develop indications for the administration of accompanying therapy in TB patients. The aim of this study was to identify the difference in the range of comorbidities between patients with MDR-TB and XDR-TB and assess the impact of comorbidities on TB treatment. Materials and Methods: A retrospective, prospective study was conducted where 307 patients with MDR-TB and XDR-TB pulmonary tuberculosis aged 18 to 75 years who received eTB treatment from 2016 to 2021 in St. Petersburg hospitals were analyzed. The analysis showed that the comorbidity level in MDR-TB and XDR-TB patients with TB treatment success and treatment failure was comparable with the use of the Charlson Comorbidity Index (CCI). The CCI demonstrated declining data in terms of TB treatment outcome period in both groups. A slight predominance of CCI score (3 to 4 points) in XDR-TB (22.7%) vs. MDR-TB (15.4%) patients was found. In the case of an TB treatment failure, the CCI level in MDR-TB vs. XDR-TB patients was characterized by a significantly higher rate of low magnitude (ranging from 1 to 2 points) in 21.1% vs. 4.5% (p < 0.05), which was higher in XDR-TB patients (ranging from 4 to 5 points, in 10.0% vs. 0, χ2 = 33.7 (p < 0.01)). Chronic viral hepatitis B and C infection, cardiovascular pathology, chronic obstructive pulmonary disease, and chronic alcoholism were found to be significant comorbidity factors that influenced the TB treatment success. Conclusions: It is evident that XDR-TB patients comprise a cohort with the most severe disease course due to comorbidities impacting TB treatment efficacy. The obtained data pointed to the need to determine comorbidity severity in patients with drug-resistant Mbt prior to administering TB treatment schemes.

Assessing regional risk of COVID-19 infection from Wuhan via high-speed rail

This paper demonstrates that transportation networks may be used to assess and predict the regional risk of COVID-19 infection from the outbreak. We use China's high-speed rail (HSR) network at the scale of prefecture level to assess, based on a probabilistic risk model, the risk of COVID-19 infection from Wuhan to the country's 31 province-level regions at the early stage of domestic spread. We find that the high-risk regions are mainly distributed along the southern half of Beijing-Hong Kong HSR line, where a large number of infection cases have been confirmed at the early stage. Furthermore, the two components of the infection risk, namely, the probability (proxied by the region's correlation with Wuhan through HSR) and the impact (proxied by the region's population with mobility), can play different roles in the risk ranking for different regions. For public health administrators, these findings may be used for better decision making, including the preparation of emergency plans and supplies, and the allocation of limited resources, before the extensive spread of the epidemic. Moreover, the administrators should adopt different intervention measures for different regions, so as to better mitigate the epidemic spread according to their own risk scenarios with respect to the probability of occurring and, once occurred, the impact.

Shorter antibiotic regimens impact the control efforts in high tuberculosis burden regions of Taiwan

OBJECTIVES

To assess the potential epidemiological impact and cost-effectiveness of shorter antibiotic regimens in high tuberculosis (TB) burden regions of Taiwan.

METHODS

This study combined the TB population dynamic model and cost-effectiveness analysis with local data to simulate the disease burdens, effectiveness and costs of hypothetical 4-month, 2-month and 7-day regimens compared with the standard regimen.

RESULTS

The main outcomes were the potential of shorter regimens for averted incidence, mortality and disability-adjusted life years, incremental cost-effectiveness ratio and net monetary benefit. Shorter regimens would lower incidence rates and mortality cases in a high TB burden region by an average of 19-33% and 27-41%, respectively, with the potential for cost-effectiveness or cost-saving. The 2-month and 7-day regimens would be more cost-effective than the 4-month regimen. The threshold daily drug prices for achieving cost-effectiveness and cost-saving for 4-month, 2-month and 7-day regimens were $US1, $US2 and $US70, respectively. Such cost-effectiveness would remain, even if the willingness-to-pay threshold was less than one gross domestic product per capita.

CONCLUSIONS

The findings support the inclusion of shorter regimens in global guidelines and regional-scale TB control strategies, which would improve disease control, particularly in settings with high rates of incidence and poor treatment outcomes.

Heterogeneous infectiousness in mathematical models of tuberculosis: A systematic review

TB mathematical models employ various assumptions and approaches in dealing with the heterogeneous infectiousness of persons with active TB. We reviewed existing approaches and considered the relationship between them and existing epidemiological evidence. We searched the following electronic bibliographic databases from inception to 9 October 2018: MEDLINE, EMBASE, Biosis, Global Health and Scopus. Two investigators extracted data using a standardised data extraction tool. We included in the review any transmission dynamic model of M. tuberculosis transmission explicitly simulating heterogeneous infectiousness of person with active TB. We extracted information including: study objective, model structure, number of active TB compartments, factors used to stratify the active TB compartment, relative infectiousness of each active TB compartment and any intervention evaluated in the model. Our search returned 1899 unique references, of which the full text of 454 records were assessed for eligibility, and 99 studies met the inclusion criteria. Of these, 89 used compartmental models implemented with ordinary differential equations, while the most common approach to stratification of the active TB compartment was to incorporate two levels of infectiousness. However, various clinical characteristics were used to stratify the active TB compartments, and models differed as to whether they permitted transition between these states. Thirty-four models stratified the infectious compartment according to sputum smear status or pulmonary involvement, while 18 models stratified based on health care-related factors. Variation in infectiousness associated with drug-resistant M. tuberculosis was the rationale for stratifying active TB in 33 models, with these models consistently assuming that drug-resistant active TB cases were less infectious. Given the evidence of extensive heterogeneity in infectiousness of individuals with active TB, an argument exists for incorporating heterogeneous infectiousness, although this should be considered in light of the objectives of the study and the research question. PROSPERO Registration: CRD42019111936.

Quantifying TB transmission: a systematic review of reproduction number and serial interval estimates for tuberculosis

Tuberculosis (TB) is the leading global infectious cause of death. Understanding TB transmission is critical to creating policies and monitoring the disease with the end goal of TB elimination. To our knowledge, there has been no systematic review of key transmission parameters for TB. We carried out a systematic review of the published literature to identify studies estimating either of the two key TB transmission parameters: the serial interval (SI) and the reproductive number. We identified five publications that estimated the SI and 56 publications that estimated the reproductive number. The SI estimates from four studies were: 0.57, 1.42, 1.44 and 1.65 years; the fifth paper presented age-specific estimates ranging from 20 to 30 years (for infants <1 year old) to <5 years (for adults). The reproductive number estimates ranged from 0.24 in the Netherlands (during 1933-2007) to 4.3 in China in 2012. We found a limited number of publications and many high TB burden settings were not represented. Certain features of TB dynamics, such as slow transmission, complicated parameter estimation, require novel methods. Additional efforts to estimate these parameters for TB are needed so that we can monitor and evaluate interventions designed to achieve TB elimination.

A pulmonary tuberculosis outbreak in a long-term care facility

In long-term care facilities (LTCFs), the elderly are apt to be infected because those with latent tuberculosis infections (LTBIs) are at an increased risk for reactivation and post-primary TB disease. We report an outbreak of TB in staff and residents in a LTCF. An outbreak investigation was conducted after two TB cases were reported from the LTCF. A tuberculin skin test (TST), bacteriological examination and chest radiograph were administered to all facility staff and residents. An outbreak is defined as at least two epidemiologically linked cases that have identical Mycobacterium tuberculosis genotype isolates. This outbreak infected eight residents and one staff member, who were confirmed to have TB in a LTCF between September 2011 and October 2012. Based on the Becker method, the latent and infectious periods were estimated at 223·6 and 55·9 days. Two initial TST-negative resident contacts were diagnosed as TB cases through comprehensive TB screening. Observing elderly people who have a negative TST after TB screening appears to be necessary, given the long latent period for controlling a TB outbreak in a LTCF. It is important to consider providing LTBI treatment for elderly contacts.

Aerosol-Transmitted Infections-a New Consideration for Public Health and Infection Control Teams

Since the emergence of the 2003 severe acute respiratory syndrome (SARS), the 2003 reemergence of avian A/H5N1, the emergence of the 2009 pandemic influenza A/H1N1, the 2012 emergence of Middle East respiratory syndrome (MERS), the 2013 emergence of avian A/H7N9 and the 2014 Ebola virus outbreaks, the potential for the aerosol transmission of infectious agents is now routinely considered in the investigation of any outbreak. Although many organisms have traditionally been considered to be transmitted by only one route (e.g. direct/indirect contact and/or faecal-orally), it is now apparent that the aerosol transmission route is also possible and opportunistic, depending on any potentially aerosol-generating procedures, the severity of illness and the degree and duration of pathogen-shedding in the infected patient, as well as the environment in which these activities are conducted.This article reviews the evidence and characteristics of some of the accepted (tuberculosis, measles, chickenpox, whooping cough) and some of the more opportunistic (influenza, Clostridium difficile, norovirus) aerosol-transmitted infectious agents and outlines methods of detecting and quantifying transmission.

Cost-effectiveness of adding bedaquiline to drug regimens for the treatment of multidrug-resistant tuberculosis in the UK

OBJECTIVE

To evaluate the cost-effectiveness of adding bedaquiline to a background regimen (BR) of drugs for multidrug-resistant tuberculosis (MDR-TB) in the United Kingdom (UK).

METHODS

A cohort-based Markov model was developed to estimate the incremental cost-effectiveness ratio of bedaquiline plus BR (BBR) versus BR alone (BR) in the treatment of MDR-TB, over a 10-year time horizon. A National Health Service (NHS) and personal social services perspective was considered. Cost-effectiveness was evaluated in terms of Quality-Adjusted Life Years (QALYs) and Disability-Adjusted Life Years (DALYs). Data were sourced from a phase II, placebo-controlled trial, NHS reference costs, and the literature; the US list price of bedaquiline was used and converted to pounds (£18,800). Costs and effectiveness were discounted at a rate of 3.5% per annum. Probabilistic and deterministic sensitivity analysis was conducted.

RESULTS

The total discounted cost per patient (pp) on BBR was £106,487, compared with £117,922 for BR. The total discounted QALYs pp were 5.16 for BBR and 4.01 for BR. The addition of bedaquiline to a BR resulted in a cost-saving of £11,434 and an additional 1.14 QALYs pp over a 10-year period, and is therefore considered to be the dominant (less costly and more effective) strategy over BR. BBR remained dominant in the majority of sensitivity analyses, with a 81% probability of being dominant versus BR in the probabilistic analysis.

CONCLUSIONS

In the UK, bedaquiline is likely to be cost-effective and cost-saving, compared with the current MDR-TB standard of care under a range of scenarios. Cost-savings over a 10-year period were realized from reductions in length of hospitalization, which offset the bedaquiline drug costs. The cost-benefit conclusions held after several sensitivity analyses, thus validating assumptions made, and suggesting that the results would hold even if the actual price of bedaquiline in the UK were higher than in the US.

Modeling the spread of tuberculosis in semiclosed communities

We address the problem of long-term dynamics of tuberculosis (TB) and latent tuberculosis (LTB) in semiclosed communities. These communities are congregate settings with the potential for sustained daily contact for weeks, months, and even years between their members. Basic examples of these communities are prisons, but certain urban/rural communities, some schools, among others could possibly fit well into this definition. These communities present a sort of ideal conditions for TB spread. In order to describe key relevant dynamics of the disease in these communities, we consider a five compartments SEIR model with five possible routes toward TB infection: primary infection after a contact with infected and infectious individuals (fast TB), endogenous reactivation after a period of latency (slow TB), relapse by natural causes after a cure, exogenous reinfection of latently infected, and exogenous reinfection of recovered individuals. We discuss the possible existence of multiple endemic equilibrium states and the role that the two types of exogenous reinfections in the long-term dynamics of the disease could play.